Second Chance
by Beaker Bait
Summary: In the future where things aren't going so well in the fight against the Wraith, one man is given the chance to change all that, but will he take it?
1. Anniversary

Title: Second Chance.

Summary: In the future where things aren't going so well in the fight against the Wraith, one man is given the chance to change all that, but will he take it?

Parings: Shep/Weir for sure. There are others hinted at or mentioned, but not vitally big in the story.

Spoilers: Anything from season one and two is fair game. But some spoilers for _'Allies' _are most likely the only ones. There are a few SG-1 spoilers here and there, but nothing real big.

Warnings: Some language.

Disclaimer: Stargate Atlantis is not mine. Only the story line and any made up characters that may appear in the story belong to me.

A/N: Ok parts of this story can be blamed on watching too much of 'Charmed' season six. A friend of mine just got the DVD box set and insisted on a continuous all weekend viewing marathon. So don't be surprised if parts of this story seem familiar, I'm sure several things from that season sunk into my subconscious and bled out while I wrote this story, despite my best efforts to not let that happen. All credit goes to the creators of 'Charmed' for those sections.

* * *

Stepping out of the Central Command building Major Troy Sheppard lifted the collar of his jacket up in an attempt to keep the rain out. God he hated this godforsaken planet, it rained for nearly ten months out of the year and was scorching hot for the other two. Ever since the Wraith had finally managed to break through Earth's defenses four years ago and lay siege to the planet the small handful of survivors - little more than a thousand people - had been forced to move from planet to planet trying to stay one step ahead of them. 

The "Alpha Site" wasn't much to look at, there was only one actual building - Central Command - that acted like a mini SGC; the military used it as their base of operation, the Stargate was held there and the scientists study any technology that might be used in the war against the Wraith there. Everything else used as shelter was either a tent or some kind of natural shelter that could be found on whatever planet they were on, like caves and such.

There was one large tent set up as a communal shower, another large one served as the Med tent, and a slightly smaller one was used as the Mess tent. Military personnel either lived in the few rooms that were available in the Central Command building or the barrack tents - half circling the perimeter of the settlement, the other half circling Central Command. The rest of the tents were for the civilians to live in.

Heading for the Mess tent Troy passed the Med tent. Stopping he took a moment to close is eyes in reverence for those unlucky enough to end up in that tent. With supplies running low and medical personnel in even shorter supply few people survived the Med tent these days. Troy didn't envy Carson or Dr. Lam their jobs one bit.

Medical supplies weren't the only thing they were low on these days, food was also starting to become an issue. Lately it seemed almost impossible to find another world that hadn't been touched by the Wraith and wasn't suffering like they were. They hadn't heard from the Tok'ra or the Asgard in years and it had been over a month since they'd last heard from the Daedalus; things were beginning to look really bad for the human race.

Moving on he spotted a group of the younger children playing out in the rain in blissful ignorance while their parents tried to round them up and get them out of the rain. Troy suddenly found himself longing for the days when he'd also held such blissful ignorance; the days before his mother had passed away and he and his father had started to grow apart, the days before the Wraith had come and destroyed Atlantis.

Entering the Mess tent Troy spotted Carson and Radek sitting at one of the tables at the back of the tent. Making his way over he plopped down into an empty chair pouring himself a glass of Radek's latest batch of home made hooch. They may not of had much of anything else but they did have plenty of Radek's home made brew - he was always working to prefect it, saying that he didn't have much else to do these days since engineers weren't all that high in demand.

"Carson, Radek." He greeted as he took a drink.

The two older men nodded their heads in greeting as they drank from their own glasses. The three men sat silently waiting for the final two people of their group to arrive. When Nathan McKay and his mother Kate arrived Troy filled the last two glasses on the table and slid them over to the two.

"Hard to believe it's been ten years." Radek, his tone soft, broke the silence a moment later.

"Aye it feels like just yesterday we were all there." Carson agreed, taking a sip of his drink.

The group fell silent again as they each got lost in their own thoughts. Every year for the last ten years, no matter what, the five gathered together to mark the anniversary of the destruction of Atlantis at the hands of the Wraith. Out of the hundreds of people that had been living in the city only a small handful had managed to make it through the gate back to Earth.

They had all lost loved ones that day; Radek his fiancé, Carson his wife and daughter, Nathan his father, Kate her husband, and Troy his father - although he had to admit he wasn't as broken up about that one as much as he probably should have been, he and his dad hadn't been all that close.

"To the fallen." Nate lifted his glass.

"May their sacrifices never be in vein." Troy added raising his own glass.

"The fallen." The others raised their glasses as well. The group passed the night away reminiscing about old times while drowning their sorrows in Radek's hooch.

* * *

Groaning Troy rolled over on his cot as the voice coming from his radio penetrated his alcohol muddled brain. Reaching towards the nightstand he cursed when he didn't find his earpiece where he normally left it at night. Slowly sliding off the cot Troy began searching the piles of clothing that had accumulated on his floor - he probably should really do some laundry sometime soon. 

Finally finding the offending earpiece he put it on. "This better be the world is gonna end right this second important, other wise I'm going back to bed. It is my day _off_ after all." He croaked out, his mouth and throat feeling like a desert.

"I'm well aware of that Major." The voice of General Landry came over the radio. "And I wouldn't be bothering you, but we have a security breach in one of the lower labs and at the moment next to me you're the highest ranking officer planet side." Not that, that was saying much there was only Colonel Carter and Colonel Mitchell between Troy and Landry rank wise.

It was then that Troy became aware of the intruder alarm sounding, which only added to the pounding in his head. Mentally groaning Troy pulled himself up and started getting dressed, "I'm on it sir." He disconnected his radio and started looking for his gear.

* * *

Damn his head was killing him, Troy thought as he advanced on his target. There was a reason he always requested the day after the anniversary off. But did whoever the hell had broken into the lab give a damn that Troy was sporting the hangover from hell? Apparently not judging by the fact that the intruder alarm was still going off. Troy really wished somebody would turn the damn thing off. 

Consulting his Life Signs Detector Troy was grateful to see that the lone dot was still in the same lab it had been for the last ten minutes. Signaling for the two men with him to hold by the door Troy slowly entered the lab only mildly surprised to find that he recognized the intruder. The man's name was Dr. Brad Jamas, he'd worked at the SGC as one of the many scientists there since the SGC had first been established. After his entire family had been taken when the Wraith attacked Earth Jamas had been forced to take a leave of absence due to mental stress - not that Troy could fault they guy, he knew what it was like to loose people you cared about to the Wraith.

Seeing what Jamas was working on Troy tensed raising his weapon. The man was standing at the control panel for the Ancient time machine that had been found off world the month before - Troy only briefly paused to wonder how Jamas even knew about the thing, let alone work it, the machine wasn't general knowledge to the settlement. The team that had found the machine learned that an Ancient named Janus had been the one to create the device. Troy remembered Rodney once telling him about the older Dr. Weir they'd found in Atlantis - Janus obviously hadn't stop his research and had found away to create a time machine with out the aide of a Jumper.

"Back away from the panel, Jamas." Troy ordered.

"I'm afraid I can't do that, Major." Jamas paused, but didn't move away from the machine.

"And I can't let you use that machine."

"It's the only way to stop the Wraith."

Troy was beginning to get an idea of what Jamas was planning. Command had already thought of using the time machine against the Wraith, but had just as quickly discarded the idea. In order to power the time machine a ZPM was needed and the one hooked up to it was almost completely out of power. Most of the scientists were convinced that the ZPM didn't even have enough power to send a person back in time even once, let alone the power to bring that person back to the present.

"Yeah and how do you plan on doing that?" Troy questioned hoping to keep Jamas distracted while he moved closer.

"By going back to the beginning and stopping this war before it ever has the chance to start." Jamas quickly hit a button on the panel causing a portal to suddenly form in the middle of the room. So much for the ZPM not having enough power.

Troy was slightly startled by the sudden appearance of the portal – it reminded him of the event horizon of a Stargate but with out the Stargate. Taking advantage of Troy's moment of distraction Jamas bolted for the portal.

"Shit," Catching sight of Jamas moving for the portal Troy lunged at the man trying to stop him. Jamas quickly angled his body so that when Troy slammed into him the Major's momentum pushed them into the portal.


	2. Time Travel

Tempe: This one's for you. It's people like you that make a writer want to stick with a story to the end. And as for the whole killing off thing I think it depends on the author. For meI think it adds the potential for angst, which it definitely will in this story

* * *

Waking slowly John stretched, tightening his hold on Elizabeth as he kissed her bare shoulder. Sighing contently Elizabeth snuggled closer to John softly kissing his chin then rested her head against his chest. 

"We should be getting up." Elizabeth spoke up having caught a glance of the clock on John's bedside table.

John groaned, reluctant to let her go. "Take a sick day, leave Rodney in charge for the day."

"And risk having a mutiny on my hands, I think not." Elizabeth began to pull out of his arms. Growling in frustration John reluctantly let her go, burrowing deeper under the covers as she disappeared into the bathroom.

Moments later Elizabeth reappeared looking ready for the day. Smiling she bent over to kiss John's temple while attempting to pull the covers off of him. "Come on sleepy time to get up."

"But I don't wanna go to school today, mommy." John teased as he rolled over pulling Elizabeth down next to him. Draping an arm over her waist he burrowed his head into her side.

"_Elizabeth."_

Rodney's voice coming from Elizabeth's radio caused John to groan again. "Don't answer."

She smiled running her fingers through his hair. "Go ahead Rodney."

"_We just picked up a strange energy reading emanating in the gate room."_

"Do you know what's causing it?" Elizabeth's fingers paused, while John lifted his head paying attention.

_"Not yet."_

"I'll be right there." She started to pull out of John's arm.

"_You might want to bring John with you just in case."_

Before Elizabeth could respond to Rodney's last statement he disconnected his radio. "I think he suspects something's going on between us." She looked down at John.

"Him along with everyone else in this city." He smirked when she raised a questioning eyebrow. "Let's just say certain people aren't as discrete about their betting as they'd like to think. Maybe we should officially let people know and put them put of their misery. Besides…" He paused to caringly kiss the slight bulge that was beginning to show on her stomach if you knew to look for it. "The cat's gonna be out of the bag soon any way."

"Later, right now we have work to do." Elizabeth stood up holding her hand out to John. Sighing John forced himself out of bed. Five minutes later he was ready to go and the two headed for the control room.

* * *

Working at one of the consoles in the control room trying to figure out what the strange energy reading was Rodney was surprised when out of nowhere something that looked like the event horizon of a Stargate appeared in the gate room. Moving to the balcony over looking the gate room he watched as two bodies appeared. 

One moment Troy had been in one of the labs then the next thing he knew he was in the Atlantis gate room. Not having expected to suddenly be in Atlantis suspended several feet above the floor Troy didn't have time to brace himself for when his body realized that no it couldn't defy gravity and slammed into the ground.

Landing hard on his right side he lost hold of his P-90, it sliding across the floor. Seeing the weapon Jamas quickly attempted to scramble to his feet as he dived for it. Troy also made a dive for the weapon. Struggling with Jamas, Troy felt his head slammed into the hard floor, blackness threatening the edges of his vision.

Taking advantage of the moment Jamas reached out frantically with his right hand, and felt cool metal under his fingers. Shaking off the nausea swirling in his gut, Troy saw his P-90 in Jamas' hands and just barely had enough time to scramble to his feet and take refuge behind one of the large shipping crates in the room as a bullet whizzed past. Thank God they'd arrived at a time right after the Daedalus had made a supply run.

Quickly pulling out his 9mm Troy poked out from around the crate and returned his own shot. Jamas hurriedly took cover behind another shipping crate. Ignoring the guards and surprised scientists in the room Troy carefully moved from the crate he'd been hiding behind to another one hoping to get a clean shot at Jamas.

"Give it up Sheppard!" Jamas called out making his own way through the shipping crates.

"What would be the fun in that?" Troy called back as he registered in the back of his mind the doors to the gate room opening and John and Elizabeth entering the room.

"Don't you understand? This is the only way to stop the Wraith from reaching Earth. As long as this city exists Earth is in danger."

Suddenly it hit Troy like a ton of bricks just what exactly Jamas was planning to do. "I'm not going to let you destroy this city and kill hundreds of innocent people Jamas."

Noticing Elizabeth in the gate room Jamas knew what he had to do. "You're a good guy Sheppard and I wish it didn't have to be this way, but I don't have a choice." Breaking from his cover Jamas took aim at Elizabeth.

Catching sight of Jamas breaking cover and aiming for Elizabeth, Troy got a knot in his gut. If he was right about what time period Jamas had brought them to, Elizabeth – his mother – would be about three or four months pregnant with him, meaning that if Jamas killed her Troy would cease to exist.

Immediately he lunged from his own cover pointing and firing his 9mm at Jamas as he pushed Elizabeth out of the way, once again slamming into the ground this time on his left side. Troy held still for a moment never taking his eyes or gun off of Jamas who was now sprawled out on the ground. Satisfied that the man wasn't getting immediately up Troy pushed himself up and cautiously approached Jamas.

Looking down at the man Troy could tell he was dead. Sighing he closed his eyes briefly as he kneeled next Jamas, before he started searching him for the remote device that would allow Troy to return back to his own time. Finally finding it he cursed as he held it up seeing the nice little bullet sized hole through the middle of it.

As they'd entered the gate room both Elizabeth and John had been surprised to find two strangers in the middle of a stand off, before either of them had had a chance to find out what was going on one of the men probably in his late forties with graying hair left his cover and took aim at Elizabeth.

Before John could even think to react the other man looking to be in his mid-twenties with black hair was pushing her out of the way firing at the other man. While the younger man cautiously moved towards the older man John instantly dropped next to Elizabeth making sure she was ok.

"I'm fine." Elizabeth pushed herself up taking the hand John offered her.

Nodding he pulled his 9mm out of the holster on his leg turning his attention to the stranger. By now the guards in the room had regained their senses and had their weapons trained on the intruder.

"Put your gun down and stand up slowly." John ordered. The man may have just saved Elizabeth from being shot, but that didn't mean John trusted him.

Hearing the sound of his father's voice Troy tensed as he cautiously raised his arms up wincing at the twinge of pain in his shoulders. As he started to come down from his adrenalin rush, Troy took note of the increased pounding in his head, most likely a concussion from when Jamas had bounced his head off the floor added to the hangover he was still feeling.

Slowly standing up he suddenly felt light headed and a bit dizzy, he wobbled on his feet for a second before falling back down to his knees. Yeah definitely a concussion.

"Note to self: standing is bad." Troy mumbled to himself. Closing his eyes briefly he fought down the nausea before opening them again.

"Who are you?" John demanded, only briefly registering in the back of his mind Elizabeth requesting Carson's presence in the gate room.

"I probably shouldn't tell you that." Troy answered as he watched Elizabeth move to stand next to John while Rodney started down the stairs from the control room.

"Why not?" Elizabeth questioned this time.

Troy paused as Carson entered the gate room followed by Ronon and Teyla who had come to see what all the fuss was about. "Because it could change everything. I came here to stop him," He indicated Jamas. "Not change the future..." He trailed off a moment as he looked at the Ancient remote still in his hand. "But since my only ticket home for the moment is out of commission I'm gonna be stuck here for a while and I guess you people need something besides 'hey you' to call me. So call me Troy."

"Alright Troy," Elizabeth nodded her head slightly. "I'm Dr.--"

"I know who you are..." Troy cut her off. Uncertainty and hesitation flashed in his eyes as if he wasn't quite sure how to address her. "Dr. Weir. I know who all of you are."

"Carson, Rodney." Troy briefly turned his attention to the two men, his eyes filled with caring and affection.

"Teyla, Ronon." He nodded his head slightly, admiration and respect shinning in his eyes. "It's good to see you guys again." He hadn't seen them since just before the Wraith had attacked the city, the two had been off world when the city had been unexpectedly attacked and Troy had never found out what had happened to them.

Last Troy turned his attention to John, "Colonel Sheppard." Troy's tone was clipped and professional. It was hard to miss the flash of anger that passed through Troy's eyes.

"Have we met you before?" Looking at the young man Elizabeth had the strangest feeling that she knew him some how, had some kind of connection with him.

"No, not yet."

"Wait," Rodney spoke up snapping his fingers as something suddenly clicked in his mind. "That man he called you Sheppard earlier..."

"Damn, I was hoping nobody caught that." Troy's glance shifted to the ground briefly. "You're right Rodney he did, that's because my last name is Sheppard."

"Sheppard as in...?"

"As in Colonel Sheppard, yes. He and Dr. Weir are my parents...or more accurately will be in about another six months."

"Wait six…then that means…that you're…" Rodney pointed at Elizabeth, then at John. "And that you…"

"See I told you the cat would be out of the bag soon." John leaned over to whisper to Elizabeth as Rodney tried to form a complete sentence.

Elizabeth remained silent for the moment studying Troy's features. He definitely had John's hair and jaw line. John also studied his "son's" features, it was easy to see that the young man was Elizabeth's child; the nose, the eyes, the ears, and the mouth they definitely all came from Elizabeth.

"Congratulations Dr. Weir, Colonel Sheppard." Teyla spoke up before Rodney got over his shock and went off on one of his rants - it was one thing to suspect a relationship between the two leaders, but another to actually know. Ronon just nodded a hint of a knowing smirk on his face. Everyone else in the room - with the exception of Carson who already knew all this, he was the one to tell the woman she was pregnant after all - was too stunned to say anything.

"So why did this guy..." John deciding it was time to get back to more important topics pointed at Jamas.

"Jamas, Dr. Brad Jamas." Troy supplied.

"Right. Why did he come here?"

"To try and change the future by destroying Atlantis."

"Why would he want to do that?" Rodney had regained his composure.

"Can't tell you that."

"What? Why not?"

"Because I didn't come here to change history..." Troy trailed off a moment as a small wave of dizziness washed over him reminding him of the pounding in his head.

Seeing Troy go slightly pale as he wavered a bit Carson quickly stepped forward, kneeling next to Troy to give him a once over. "How's the head doin' Lad?"

"Feels like it's gonna explode, but whether that's from the concussion or the hangover from Radek's latest batch of hooch I couldn't tell ya." Troy answered as he forced himself up into a standing position, ignoring Carson's attempt to keep him down.

Carson frowned slightly turning his attention to Elizabeth and John, "I think more questions can wait, right now I want him in the infirmary."

"Relax I'm fine Carson. It'll take more than a hangover and having my head bounced off the floor to keep me down."

"Well if there was any doubt before." Carson softly muttered as he started steering Troy out of the room. "I don't care how you _think_ you're doin' you're going down to the infirmary and that's finale." He spoke louder that time.

* * *

Half an hour later John and Elizabeth sat in Carson's office waiting for the doctor to finish examining Troy. Looking through the window to where Troy was sitting on one of the infirmary beds Elizabeth sat absently running a hand over her stomach. She was still trying to wrap her mind around the fact that the young man sitting out there was the child currently growing inside of her. 

"Here," John handed Elizabeth a cup of tea as he sat down next to here. "It's weird isn't it."

"Mmm..." Elizabeth took the cup and breathed in the sweet aroma. "It's hard to believe that the child growing inside me will one day grow up to be that man out there."

The two fell into a comfortable silence before Elizabeth spoke up again. "I'm worried about him." She placed the cup down, taking one of John's hands and holding it against her stomach.

"How so?" John used his free hand to rub her back.

"The way he acted towards us. With the others he seemed so warm and open, you could see the care and affection shining in his eyes. But with us it was different, he was hesitant and unsure when talking to me and with you he was distant and professional almost coldly so. And you can't tell me you didn't notice the anger that flashed through his eyes when he looked at you."

"Yeah I noticed." John whispered as Elizabeth rested her head on his shoulder. He understood her concerns, they were the same ones that had been running around in his head.

Before anything more could be said Carson finally entered the office. "You'll be pleased to know that he'll live. Aside from a minor concussion and being slightly undernourished and dehydrated he's fine. Nothing some rest and a good meal or two can't take care of. I've started him on an IV for the dehydration just to be safe."

"Can we see him?" Elizabeth lifted her head from John's shoulder.

"I'm afraid that will have to wait 'til tomorrow. He's sleeping right now and I don't want to disturb him. I slipped him a slight sedative to make sure he actually slept." Carson wasn't an idiot - Troy was a Sheppard after all - there was no way he was taking the chance that the man was just like his dad when it came to staying in the infirmary.

Knowing that Carson wasn't likely to let them stay in the infirmary until Troy woke up John took Elizabeth's hand and led her out of the infirmary hoping to find something to take their minds off of the young man sleeping in one of the infirmary beds.


	3. Memory

A/N: Gets all warm and fuzzy from the love. You guys really know how to make an author feel loved.

* * *

Waking up the first thing Troy became aware of was the nasty case of cotton mouth he had going. The next thing was Carson hovering over him fiddling with the IV in the back of his hand. It took a moment for his mind to catch up but soon the previous days events came flooding back. 

"You spiked my IV." It was a statement not a question.

"Aye I did. It was the only way to make sure that you actually slept instead of trying to escape."

"Bastard." Troy tried to glare at Carson, but the slight curving of one corner of his mouth took away from the effect."Well since I'm trapped here how about some food?"

"I think I can manage that." Carson smiled as he wandered off to round up some food.

Ten minutes later Troy spotted Rodney entering the infirmary carrying a tray of food. He smiled as he listened to Rodney mutter about a deranged Scotsman trying to poison his patients with the infirmary slop he called food.

"Nice to know some things never change." Troy chuckled as Rodney put the tray down and pulled up a chair.

"Just be glad I was on my way down here to check on you or else you'd be eating that slop Carson calls food." Rodney plopped down in his chair as he swiped a fruit off the tray.

"You mean coming down here to try and pry information out of me about the future."

"I wasn't...I would never..." Rodney sputtered.

"I know you Rodney, that thirst for knowledge it's a part of who you are. Part of what makes you so fun to hang out with." Troy answered as he dug into his food. Out of the corner of his eye he caught the infirmary doors opening and Elizabeth entering, minus John - who had been called to an early meeting with Caldwell before the Daedalus left for Earth.

"Hang out? We hang out together?"

"Yeah, a lot actually, especially after Mom--" He quickly cut himself off before he reviled too much. "Let's just say we get the chance to hang out together a lot. But that was fine with me, you were cool to hang out with."

"You hear that I'm cool in the future." Rodney smiled smugly as Elizabeth stopped next to his chair.

"After Mom what?" Elizabeth questioned ignoring Rodney for the moment. She was curious about what could have happened to her that would mean him and Rodney spending a lot of time together.

"I can't talk about it. It will mess with the future."

"But you can talk about me being cool right?" Rodney was still looking smug.

"Yeah you were the best. Actually made things funner at times." Troy had to chuckle at Rodney again.

"I have to admit that kind of surprises me, cause you know I'm not really known for being all that great with kids."

"You did fine. I can't complain and I know Nate never had any complaints."

"Nate?" Rodney raised a questioning eyebrow.

"Sorry, can't." Troy shook his head turning back to his food. He couldn't remember the last time he'd had a decent meal.

The two spent the next hour talking about all kinds of things. Elizabeth had left soon after arriving when it became obvious that Troy still had that hesitant and uncertain air about him around her and that she wasn't going to get more than a one or two word answer from him about anything.

* * *

It was another day before Carson finally let Troy out of the infirmary. Walking through the corridors headed for his mom's office Troy was acutely aware of the guard that was following him from a short distance behind. While he understood why a guard had been assigned to him it still hurt slightly that his family didn't trust him - he knew logically that they had no reason to trust him, but it still hurt. 

Arriving at her office Troy stood just inside the doorway with his hands stuffed in his pockets. His parents along with Rodney were already there and were talking amongst themselves, but fell silent when he entered.

Having a pretty good idea what this meeting was about and wanting to get it done and over with Troy spoke first. "Ok look here's the deal, I'm from around twenty four years into you future and no I won't tell you anything specific about what is going to happen in those years because I don't want to risk changing the future and possibly making things worse than they already are."

"Fair enough." Elizabeth nodded her understanding.

"Aren't you a little young to be a major already?" John spoke up.

Troy just shrugged, "High demand, short supply when it comes to officers."

"Will you at least tell us how you got here so that we could possibly find away to get you back to your time period?" At the moment Elizabeth didn't care about military logic or anything to do with the military period at that moment. She was more curious about the person behind the rank.

"Ancient technology brought me here. You all know about the Ancient called Janus," The others nodded their heads. "Well as I'm sure you've already guessed he didn't stop his research into or experimenting with time travel. About a month ago - my time - an off world team find a device created by Janus that allowed a person to travel through time with out the aide of a jumper."

"How was this person supposed to get back then?" Rodney questioned interested in hearing about the device.

"With this," Troy pulled the Ancient remote out of the vest he was still wearing - minus any weapons. "But as you can see the nice little bullet shaped hole through the middle of it makes it useless to me."

"So how are we supposed to get you back to your time, with out that?" John inquired this time.

"Solar flares."

"Solar flares?" John had no idea where he was going with this.

"Yeah, it's happened before with SG-1. They went through a wormhole that passed through a solar flare and ended up in 1969. Got back the same way."

"Slight problem with that plan, we don't have the technology to predict solar flares." Rodney pointed out.

"No, but the Ancients do. Unfortunately the astrology lab is located in a section of the city that was heavily damaged by that super storm you guys had last year and haven't been able to repair yet. Besides it would take months to repair and get the lab running, which is why I..." He pulled some papers from his vest and handed them to Rodney. "Printed these off of my PDA last night. They're plans for a generator that can simulate the effects of a solar flare on the Stargate. The scientists at the SGC worked on it off and on for years. It's not quiet finished but close enough I think that your scientists can finish it hopefully."

Troy had to send a silent thank you up to whoever had thought that it would be a good idea to have all off world soldiers carry PDA's with what was saved from the SGC computer systems before the evacuation of Earth downloaded onto them using, ironically, Rodney's data compression program. In the beginning the higher ups had been afraid of what might happen if a PDA fell into the wrong hands but that had quickly been taken care of; to access the information a finger print and retina identification scan was required along with a number of different passwords and the ultimate failsafe a specially designed virus to wipe the entire hard drive if someone with out authorization attempted to access the PDA.

"This could actually work." Rodney muttered as he studied the plans. "We should be able to use the readings we took when you arrived to make the calculations needed to send you back to your time. We just have to get the generator working, which shouldn't be too hard most of the hard stuffs been done already."

"Get to work on it." Elizabeth barely finished speaking before Rodney was out the door headed for his lab.

"If there's nothing else...?" Troy questioned not really looking at either of his parents.

"No, I guess that's all for now." Nodding his head Troy left the room a small part of him silently thankful to be out of there.

It was strange seeing his parents again. Troy hadn't seen his mom since she'd passed away when he was six and honestly he couldn't really remember all that much about her- mostly just the pain of losing her - she was practically a stranger to him, which made it kind of awkward for him to be around her because he was never quite sure how he was supposed to act.

And his dad...his dad _was_ a stranger to him. If it weren't for the fact that he'd lived with the man for fourteen years and been told repeatedly that_ yes_ John was his father, Troy would have sworn the man was just another person living in the city. Ever since his mom had died his dad had pulled away from his son had never allowed him to get close. Growing up Troy had always felt like his dad didn't want to be around him, that his job was more important and always came first. In away Rodney had been more of a father to him than John ever had.

* * *

_The city was shaking under the relentless bombarded of the Wraith Hive ships in orbit around the planet. The Wraith had arrived in overwhelming force several hours ago and had been continuously attacking Atlantis non-stop. For most of the attack the Wraith had managed to disable the gate preventing Atlantis from dialing out. By the time they were able to by pass the problem and dial out more than half the city was in ruins and hundreds were dead. When it become obvious that they weren't going to win this time the evacuation order had been given. _

_Running down the corridor towards the gate room as fast as he could Troy made sure he checked every room along the way for stragglers - not that he expected to find any of those - or injured that couldn't make it to the gate on their own. By now most of the survivors had been sent through the gate the only people that remained were mostly soldiers and the last group waiting to go through the gate. Finding a young Athosian girl huddled in a corner holding her ankle Troy quickly scooped her up and continued to the gate room._

_"Rodney come on we gotta go!" Troy hollered when he entered the gate room seeing Rodney still in the control room working furiously at one of the consoles. Passing the girl off to one of the scientists going through the gate Troy started up the stairs._

_"Troy what are you still doing here?" Rodney demanded as Troy grabbed his arm and started ushering him down the stairs. "You were supposed to have gone through the gate already with the other kids."_

_"Someone had to make sure you didn't do something stupid like get yourself killed."_

_The two reached the bottom of the stairs just as a group of Wraith soldiers burst into the room. Immediately Rodney put himself between the Wraith and Troy, pushing the boy back towards the gate. The few soldiers in the room began firing as they backed towards the gate herding the remaining civilians through._

_In the chaos Troy briefly lost sight of Rodney. When he finally spotted him again Troy was horrified to see that one of the Wraiths had a hold of him. He tried to get to Rodney and help but one of the soldiers grabbed him and started trying to force him through the gate. Troy put up one hell of a fight but in the end it wasn't enough. The last thing he saw before being pushed through the gate was the Wraith beginning to feed on Rodney..._

Jolted into wakefulness, Troy sat up in bed as the images from his nightmare flooded his mind. It had been a long time since he'd last had that dream, but he still remembered it like it was yesterday. They'd lost of lot of good people that day his father and Rodney among them. The only thing he'd been even close to thankful for that day was that Kate and Nathan had been among one of the first groups evacuated so they didn't have to see Rodney die - Troy only wished he'd been so lucky. As for his dad Troy wasn't sure what had happened to him exactly the last he'd seen of him the man was rushing off down a corridor with a group of soldiers headed for a group of Wraith that had gotten into the city.

Knowing that he wasn't going to get any more sleep Troy slid out of bed noticing that it was early morning and that the sun was only just starting to raise. Pulling on some clothes he made his way down to the gym. He wasn't surprised to find the place empty at that time of morning - even Ronon wouldn't be there for at least another hour.

Slipping off his shirt and shoes Troy grabbed one of the wooden staffs. He had always found that he preferred the longer staffs to the shorter Athosian fighting sticks. Taking a ready stance he closed his eyes and breathed deeply to slow his heart. Finding his center Troy began to move, he twirled the staff using fingers and arms, around his shoulders and in sweeps. Blows and blocks, offense and defense flowed into continuous motion. The staff became an extension of his own body.

The staff wove complex patterns through the air as his tension drained away. Second after second he continued to move gracefully the patterns becoming more and more complex. The movement ended abruptly with Troy bring the staff to rest against Ronon's throat. The runner had entered the room soundlessly moving to watch the younger man's movements. He hadn't even been aware that Troy knew he was there until the staff came to rest against his throat.

"Not bad." Ronon grunted his approval.

"I had good teachers." Troy put the staff away grabbing his shirt and shoes. "Hungry." It was a statement not a question. Ronon just gave a soft snort, the beginnings of a smirk on his face as he followed Troy out of the room to the mess hall. The kid had only been in the city for little over a week and Ronon hadn't had the chance to be around him very much, but found that he liked the younger man anyway and that maybe they had a lot more in common than one might think.

* * *

Sitting in the mess hall Elizabeth was eating breakfast with Carson, since John was making the weekly supply run to the Mainland that morning. She watched as Troy and Ronon entered the mess hall and began getting their breakfast. Looking up Troy briefly caught Elizabeth's eye before diverting his gaze elsewhere as he led Ronon to an empty table. 

"He hates me doesn't he?" Elizabeth sighed as she poked at her breakfast.

Glancing up Carson caught sight of Troy sitting at another table with Ronon. "What makes you think that?" He was pretty sure he knew the answer to that already, but asked anyway.

"He's been trying avoid me since he got here. He barely looks at me or speaks to me. What could I've done in the future that was so bad that my own son treats me like a stranger?"

"I'm sure it's nothing you did. Maybe John should try talking to him."

Elizabeth gave a soft huff, "Yeah that would go over real well. Troy is even worse when it comes to John. He actively goes out of his way to avoid John, won't talk to him unless absolutely necessary, hell he can barley stand to be in the same room as John."

"Aye," Carson agreed, he'd known as soon as he'd made the suggestion it was probably a bad idea. "Maybe you should have Kate speak with him, see if she can find out what's going on with the lad."

"Maybe..." She trailed off as an idea hit here. "Or better yet I'll sic Rodney on him. Troy seems to like Rodney and gets along with him. And you know how Rodney can be when he sets his mind to something." Her mind made up Elizabeth got up to go find Rodney.

Carson had to smile softly at that, Rodney wasn't exactly known for his people skills among other things. But Troy did seem to have an ease around Rodney that he didn't quiet have with anyone else in the city, maybe it wasn't such a crazy idea to have him talk with the man.


	4. Hanging Out

Later that day Rodney was in his lab working on calculations for the generator to get Troy home. The calculations should have been done days ago, but with the threat of the Wraith Hive ship on it's way to Atlantis everybody had been so busy with trying to come up with defensive plans that the generator had gotten put on the back burner. The only reason Rodney was working on it now was because he'd hit a brick wall with the Wraith problem and needed something to take his mind off of it.

Entering the lab Troy propped himself up on one of the counters making sure he was out of Rodney's way. Concentrating on his work Rodney didn't pay any attention to Troy at first.

"Was there something you wanted or are you just here to bug me?" Rodney questioned several minutes later when Troy remained silent.

"Just watching." Troy shrugged, fiddling with a pen in his hands.

"Watching?" Rodney looked up from what he'd been working on.

"Yup, used to do it all the time when I was a kid. Never really understood what you guys were doing or talking about, but it was a place where I could think and work things out in my head. After a while you guys got so used to me being around that sometimes you'd forget I was even here. You wouldn't believe some of the blackmail material I was able to gather."

"Well since you're here you can make yourself useful," Rodney handed Troy some papers full of equations. "And work those out, save me some time. The sooner they get done the sooner we can send you home."

"And what makes you think I can do these?" Troy took the papers but didn't look at them.

"Well you are Sheppard's kid and since he's like an uber math wiz..." Rodney shrugged.

"You just assumed I was one too." Troy tossed the papers back down on the counter. "Sorry to disappoint, I may have gotten the hair but I didn't get the brains. Math is one of those things I'm never gonna fully understand, no matter how hard you try to drill it into my head. And believe me you tried."

"Ok so you don't do math and I get the feeling you're not big on the whole science thing--."

"Unless it has to do with blowing stuff up." Troy got an impish grin on his face.

Rodney just rolled his eyes in a 'it figures' kind of way. "Right, anyway. It sounds to me like we don't really have all that much in common, so how is it that we end up 'hanging out' together so much in the future?"

Troy shrugged again, "You were just always there for me when I needed someone to talk to. You always listened to me even when I didn't have anything to say."

"So let's talk." Remembering his talk with Elizabeth earlier Rodney figured now would be as good a time as any to see if he could figure out what was going on with Troy.

Sighing Troy got a knowing look on his face, "Let me guess my mom wanted you to try and see if you can find out what's going on with me."

"She's worried. The way you've been acting towards her is making her think that she's a bad mother."

"What? No…she's...she's fine..." Troy hesitated slightly not sure how to respond. He honestly didn't really remember what kind of a mother Elizabeth was, but he was pretty sure she wasn't a bad one.

"Then why are you treating her like a complete stranger."

"Because she practically is one to me!" Troy got up and started pacing. "I barely remember her. She dies, as in dead and not coming back, when I'm six." He paused with his back to Rodney when he realized what he'd just said.

"Dies...? How...?" Rodney was a bit stunned he hadn't expected to hear that.

Troy shook his head as he moved to stare out the window, "I...can't...I don't know how."

"You don't know?" He moved to stand next to Troy, resting a hand on his shoulder.

"She got sick...I don't know what it was for sure, nobody would ever tell me and eventually I stopped asking. Knowing what I know now I think it might have been cancer, but considering the fact that we were living in an alien city in another galaxy it could've been any number of things." Pulling away from Rodney he started pacing again, his thoughts wandering back to when he'd first started to realize there was something seriously wrong with his mom.

_The sound of hushed voices woke him. Sliding out of bed Troy quietly moved to his door and cracked it open slightly. He could see his parents in the living room; they were arguing again, it seemed like all they ever did anymore was argue. His mom was leaning against the back of the couch, arms folded, and his dad was tensely pacing back and forth around the room - it reminded Troy of the tiger he'd seen at the zoo pacing around in his cage last year when they'd gone to Earth for a visit._

_"Damn it Elizabeth! Why are you being so stubborn about this?" Troy could tell his dad was angry._

_"John you heard what Carson said. I'm getting sicker and there's nothing he can do for me." He could tell his mom was trying to stay calm and keep the pain and fear out of her voice._

_"I know what he said. And he also said there was a chance that if you were to go back to Earth somebody there might be able to help you."_

_"Yes, a less than one percent chance. Less than one percent. John you have to accept the fact that I'm dying and there is nothing anyone can do about it."_

_Troy felt his heart stop a deep ache forming in his chest. Finding it hard to breath he leaned his back against the wall and slid down to sit on the floor. He'd known his mom had been sick for awhile but he'd had no idea it was anything serious. Every time he'd questioned her about it she'd just reassured him that she was fine and that it was just the flu. Turning his head to look out his still cracked open door Troy watched his mom as she closed the distance between her and his dad._

_She gently cupped his face with her hands briefly kissing him before resting her forehead against his. "John please, I need you to be strong for me. I know you want me to go back to Earth and that you believe something can be done to help me, but deep down in your heart you know as well as I do that there is nothing that can be done for me. Maybe if this had been caught sooner, there might have been a better chance, but now...now I need you to please just except what your heart is telling you, I don't want what little time we have left to be filled with anger and bitterness."_

_"No, damn it!" His dad pulled away from his mom. "I refuse to except that, I will never except that. You may be ready to quit and just give up but I'm not nor will I ever be." With that his dad turned around and stormed out of the room._

_Looking at his mother Troy was stunned to see tears in her eyes. Never once in his whole life had he ever seen his mother cry. Pushing himself off the ground he quickly grabbed his favorite stuffed animal - the one Teyla had made him when he was born and always helped comfort him when he needed it - and walked out of his room. _

_Seeing his mom had curled up on the couch, a distant look on her face as she stared out the window, Troy silently moved to stand in front of her. Holding his stuffed animal out to her Troy saw the realization that he'd heard the whole conversation flash through his mom's eyes. Not saying anything herself his mom took the stuffed animal giving him a sad smile. When she opened her arms he didn't hesitate to move into them and curl up with her on the couch._

Troy shook himself out of his thoughts. "Look I've already said too much, but the point is that when this is all said and done I have to go back to where my mom isn't. It's better if I just keep my distance that way it won't hurt as much when I have to leave."

"Are you so sure about that?"

Stopping Troy sighed as he took a moment to consider Rodney's question.

Knowing that Troy was a bright guy and would come to the right conclusion on his own Rodney decided to change the subject. "Come on I'm hungry let's go see what they got in the mess hall." He gently gave Troy a shove out the door.

Headed for the mess hall the two men ran into Elizabeth on her way to the Jumper bay.

"Where have you two been all day?" Elizabeth asked out loud while she silently sent Rodney a questioning look.

Rodney gave her a reassuring smile, before turning his gaze to Troy. The two looked at each other briefly then both shrugged their shoulders at the same time.

"Just...hanging out." Rodney finally answered.

"So where ya headed?" Troy, having decided that maybe Rodney was right, asked. This was his chance to get to know his mother _personally_, not just from stories he'd been told. A chance to gain some solid memories of her, instead of the vague whispers he'd had growing up.

Surprised that Troy had actually spoken to her it was a second before Elizabeth answered. "To the Jumper bay. The Athosians found some ruins on the Mainland that John thought I might like to see."

"What? No you can't go to the Mainland." Troy protested in alarm.

"Why not?" Rodney spoke up not seeing what problem the was with Elizabeth going to the Mainland. It was good that she was getting out of the city and away from work for a while.

"Why not?" Troy turned to face Rodney. "What if something happens to her?"

"Nothings going to happen to me..." Elizabeth trailed off when Troy turned back to look at her, barely controlled panic in his eyes. "Unless you know something I don't?"

"Nothings going to happen, Troy's just being over worried." Rodney ignored the look Troy sent him.

Elizabeth didn't miss the look Troy sent Rodney, "But something is going to happen to me… eventually?" Troy's silence spoke volumes. "Does this something happen soon?"

"You know I can't tell you that."

"Right well whatever it is, it obviously doesn't happen until after you're born, so stop worrying about it for now. I'll be fine."

"Yes, mom." The reply slipped out of his mouth before he could think about it. Seeing the pleased smile on his mom's face Troy looked down sheepishly at his slip.

Rolling his eyes Rodney once again gave Troy a gentle shove to get him moving. He was hungry after all and there was supposed to be blue Jell-O today. Giving a slight shake of her head Elizabeth continued on her way to the Jumper bay to meet John.

* * *

Later that evening after returning from the Mainland Elizabeth made her way to her office to finish up some last minute work that needed to be done for the weekly status report to Earth. Entering she was surprised to find a sleeping Troy slouching on the couch - he looked as if he'd been waiting for her to get back and had fallen asleep. 

Standing in the doorway she took a moment to just watch him. He looked younger more peaceful when he was sleeping compared to when he was awake and looking like he carried the weight of the world on his shoulders. The feeling of arms wrapping around her waist from behind brought Elizabeth out of her thoughts. Knowing instantly who it was she leaned back into John's chest.

"You should follow his example and get some sleep yourself." John whispered resting his chin on her shoulder.

"Can't, have to get the weekly status report to Earth ready to send out tomorrow."

Suddenly John's entire demeanor changed as he straightened up and his hold on Elizabeth tightened. "You need to start taking better care of yourself. You can't keep pulling these all nighters, you'll run yourself into the ground..."

Turning around to face him Elizabeth studied John intently for a moment. "You know something don't you...about what's going to happen in the future?"

"I kind of over heard some of what Rodney and Troy were talking about earlier today in Rodney's lab. I didn't hear everything but what I did hear I didn't like."

About to question him on what he'd heard Elizabeth paused when she saw the pleading look in John's eyes. Nodding she reached up to kiss him briefly. "I guess the report can wait 'til morning. You go ahead, I'll be right there after I wake sleeping beauty over there and send him to a real bed."

Stealing another quick kiss John left the office. Moving over to the couch Elizabeth was about to shake Troy's shoulder when she spotted an old, worn, and tattered looking picture loosely grasped in one of his hands. Curious she gently took the photo from his hand to look at it.

She had to smile at the image captured. It was a picture of her, John, and Troy - who couldn't have been more than five. She was wearing a beautiful, but simple baby blue spaghetti strap dress while both John and Troy were looking handsome dressed up in tuxedos. In the background she could see a grinning Carson - also dressed in a tuxedo - his arm wrapped around a beaming Laura Cadman who looked stunning in what was obviously a wedding dress.

The picture must have been taken at the reception after the wedding cake had been cut. Cake and frosting were smeared all over Troy's face and he was in the process of giving John the same look. In one hand Troy had a piece of cake that he was shoving into John's face, while a laughing Elizabeth had a hold of the other cake smeared hand trying to wipe it off with a napkin.

Putting the picture back Elizabeth could see the ghost of a smile on Troy's face. The picture obviously brought back good memories for him and it pleased her to know that at least at one point in his life Troy had been happy and care free. Not wanting to disturb him from what happiness his dreams were bringing him Elizabeth caringly kissed his forehead, deciding that he was ok where he was for the night. Turning to leave she took one more look at the man her child would grow up to be before turning off the lights and heading for John's quarters.

* * *

Leaving the infirmary two days later Elizabeth parted ways with John who was on his way to a sparing session with Teyla. She'd been in the infirmary for a check up with Carson to make sure everything was going ok with her pregnancy. While there Rodney had come in to have an electrical burn on his hand treated - apparently the generator project wasn't going as smoothly as Rodney had first thought. She wasn't surprised when Rodney followed after her instead of John. 

"So what'd Carson say?" Rodney questioned as he tried to get a look at the ultrasound picture of the baby in Elizabeth's hands. "Everything's ok, no problems or complications? Baby's fine and healthy?"

"Of course he's healthy Rodney. You've seen him at twenty four walking around and talking." Elizabeth smiled as they reached the transporter.

"Hey you never know, a lot of things could happen between now and then."

"Stop worrying so much you're starting to sound like..." The transporter doors opened to revel Troy leaning against the opposite wall obviously waiting for her. "...Troy."

"So how'd everything go with Carson? No problems or complications?" Troy questioned pretty much asking the same thing Rodney had.

Elizabeth couldn't help but smile at that. "Well according to this you're supposed to be a girl." She held up the ultra sound picture, a playful grin on her face. Troy just mockingly glared at his mother not amused by her humor.

"You know you'd think with all the supposed advancements they're making in medicine they could take better ultrasounds." Rodney squinted his eyes studying the picture closer trying to see the baby part.

"Oh, it's this little thing--." Elizabeth started to point out the baby but was cut off by Troy snatching the photo out of her hands.

"Hey, whoa! Ya mind?" Troy's cheeks flushed in embarrassment.

"Well that just proves it, you're gonna be a great mom, Elizabeth." Rodney smirked. "The kid's technically not even born yet and you're already embarrassing the crap out of him."

Elizabeth's smile grew bigger as Troy childishly stuck his tongue out at Rodney, before turning his attention to the ultrasound in his hands. She almost laughed at the way his face scrunched up in confusion - it was a mirror image of John's confused look - as he tilted his head sideways trying to see the baby himself.

"You should stop worrying so much. Everything is going fine with little you." Elizabeth rested a hand on her stomach.

"It's not me I'm worried about, I know I turn out fine. It's you I'm worried about, I just want to make sure you're ok." Troy shrugged his shoulders as he lowered his gaze slightly.

"See if we were on Earth this would be the point where he asks for the keys to the car." Rodney joked playfully.

"More like the Puddle Jumper, and it was you I went to for that. Some times Carson if you were busy." He handed the ultrasound back to Elizabeth.

"Really? Why?"

"Why not? You're the one who taught me how to fly."

"Me?" That surprised Rodney more than anything else Troy had told him. The fact that he couldn't fly the damned things in a straight line aside Rodney assumed that John would have been the one to teach his own son how to fly.

"Yeah you get to be a pretty decent pilot in the future. It won't be long before you get the whole flying in a straight line thing down and after that it's all down hill from there."

"Why didn't your dad teach you how to fly a jumper?" Elizabeth had been thinking along the same lines as Rodney.

"Uh...let's just say he had other priorities." Troy tried to keep the anger out of his voice. Judging by the look his mother gave him he hadn't quiet succeeded.

"What does that mean?"

"I'd rather not talk about it." Pushing off the wall Troy quickly stepped into the transporter, hitting a random spot on the map before Elizabeth could ask anymore questions.

Letting out a sigh Elizabeth shook her head slightly. Troy definitely had some issues with John that needed to be worked out, but for the life of her she had no idea about how to help the two.


	5. Confrontation

Standing in the shadows at the back of the control room Troy watched as Elizabeth spoke with the Wraith known as Michael. He'd known this day and the events that followed were coming since he'd first arrived several weeks ago. It was the actions that took place over the next couple of days that would lead to the eventual downfall of Earth.

Troy had been hoping that Rodney would have finished the generator and sent him home before the Wraith Hive ship showed up, but unfortunately seeing the Wraith as the bigger problem getting Troy back to his time period had been pushed to the back burner until after the Wraith had been dealt with.

The longer he was there the more and more he became tempted to tell his family what was about to happen. Logically he knew that he had no right to mess with the timeline, that he should just let things play out the way they were supposed to and yet at the same time he knew that Jamas had been right – his way of going about it may have been wrong, but not the _idea_ – this was the chance to end a war before it had the chance to start.

Feeling frustrated by his conflicting emotions Troy pushed off the wall he'd been leaning against and silently left the control room headed for the gym. He needed to clear his head and working out had always been a way for him to do that.

* * *

Several hours later John entered the gym intent on clearing his own head. This whole alliance with the Wraith had him on edge and he needed to sort through his thoughts before he left on the Daedalus for the trial run of the retrovirus against another Hive ship. Finding Troy there John hesitated a moment, not sure if his presence would be welcome. Even though things had been improving between Troy and Elizabeth they had remained almost hostile between him and Troy. 

"You just gonna stand there all day or what?" Troy questioned not stopping the complex looking moves he was doing with his staff.

"I don't suppose if I were to ask how this whole thing with the Wraith plays out, you'd give me an answer?" John spoke hoping to cover his surprise over the fact that Troy had actually spoken to him.

Troy didn't answer verbally just halted what he'd been doing and put the staff back with the others. Grabbing the water bottle off the bench by the window he took a long drink then made to leave the room.

"Wait," John moved to block his path. Uncertainly he held up one of his fighting sticks. "I could use a sparing partner and you look like you can hold your own."

For a minute Troy just stood there silently, then seeming to make up his mind he turned around and tossing the water bottle back on the bench he grabbed an extra pair of fighting sticks. Taking a ready stance he carefully adjust his grip, not as used to or as comfortable with the smaller fighting sticks as he was with the longer staff. Nodding John moved over to the sparing mat and just barely had the chance to get into his own ready stance before Troy took a shot at him.

It didn't take long for John to figure out that this was more than a simple friendly sparing match. Troy wasn't holding back with his hits, the younger man was out for blood. After blocking another powerful hit that had him wincing from the painful vibrations it sent through his arms John pushed off of Troy putting distance between them.

"What'd I do to make you so angry at me?" John, figuring this was probably the best chance he was going to get to get some answers, questioned. He made sure to keep just far enough away that Troy couldn't take a good shot at him.

"Why do you care?" Troy swung at John.

John was able to just deflect the swing, "I care because I'm your father and I think I have the right to know why I'm such a terrible father." Troy didn't answer just took another hard crack at John. Wincing as the shot winged his shoulder John took a shot of his own. "Deep down you hate my guts and I wanna know why."

"It won't change anything." Deflecting John's shot Troy pulled back slightly readjusting his grip on the fighting sticks.

"God you really are my son aren't you? You can be a stubborn bastard just like me when you wanna be."

That got a reaction out of Troy. Dropping his fighting sticks Troy lunged at John, shoving him up against the wall. "I am _nothing_ like you!"

"Hit a nerve did I?" John didn't try to break loose of Troy's hold.

"You're nothing but a selfish bastard." Troy punctuated the statement by punching John hard in the ribs.

The next punch hit John, square in the jaw sending him to the ground. Troy didn't stop, something inside him had snapped and now he was taking out eighteen years worth of pain and anger on John.

At that moment Elizabeth walked into the gym looking for John. She'd wanted to speak with him before he left on the Daedalus and figured he'd be in the gym. Seeing Troy hitting John she quickly rushed over and grabbed the arm Troy had raised ready to strike John again.

"Troy stop!" She ordered as she pulled him off of John. Breathing heavily Troy looked at Elizabeth then down at John. Pulling away from Elizabeth's hold Troy turned and left the gym.

Torn between going after her son and staying to make sure John was ok Elizabeth decided to give Troy a chance to cool off and kneeled down next to John. "You ok?"

"Peachy," John let his head fall back on the floor as he let out a deep sigh. "My son hates my guts and I have no idea why."

"You can't beat yourself up over this John. Whatever the reason it's in the future, which means for us it hasn't happened yet. There's still time for you to change things."

"I just wish I knew what it is that I did to make him hate me so much, so that I can change it." Letting out another sigh John forced himself up to his feet. "I'd better get going the Daedalus will be ready to go soon." He extended a hand to help Elizabeth up.

"Don't give up on him, John. You can still get through to him." Elizabeth leaned up to kiss John's cheek. "He's just being stubborn like his dad."

"Don't let him here you say that. I accused him of the same thing and well…you just walked in on how well that went over." John gave a weak smile as he kissed her forehead, before he left.

Sighing Elizabeth left the gym as well. Deciding it was time she had a chat with her stubborn son.

* * *

Sitting on one of the balconies over looking the eastern side of the city Troy carefully held the only picture he had left of his family, it had been taken when he was five at Carson's wedding. This balcony had always been one of his favorites it was the highest balcony in the city and had been the closest thing to flying Troy could get without actually leaving the ground when he was a kid. 

He heard the balcony doors open but didn't turn around already knowing who it would be. Standing in the doorway Elizabeth remained silent waiting to see if Troy would acknowledge her or not. After a moment of silence she decided that he wasn't going to make the first move.

"Want to tell me what that was all about?" She moved to sit next to her son who remained silent for several more minutes. She didn't expect to get an answer, but asked anyway on the off chance that he might let his guard down and confide in her.

"Why him?" Troy finally spoke, ignoring Elizabeth's question. "I mean out of all the people in this city you could have fallen in love with, why him? Why not Rodney, or Carson, or hell even Ronon?"

"Honestly I'm not sure I can explain it. There's just something about him that draws me to him." Elizabeth shrugged then fell silent.

"This was always my favorite spot in the whole city. I used to come out here all the time just to get away. I remember coming out here after you..." He trailed off a moment not sure if Rodney had told here anything about what they had talked about.

"Died." Elizabeth couldn't help the involuntary shiver that ran down her back. She didn't know any details but she'd been able to put things together from little hints Troy had let slip here and there.

"Yeah. Anyway I remember sitting her looking out out the view wishing I had wings so that I could fly away from here, escape from all the pain and just be free. Rodney found me here and it was like he could read my mind. Never said a word just took my hand and led me to the Jumper Bay."

"I remember sitting there on his lap, his hands wrapped around mine on the controls, wishing that it never had to end that I could stay up there forever. With Rodney I felt like everything would be ok, that he would always be there for me. Dad tried to be there for me...at first...but he just couldn't deal with me after a while. I think I reminded him too much of you. He took your death and everything that led up to it pretty hard..." He trailed off lost in his memories.

_Standing in the cemetery Troy could feel water starting to run down the back of his shirt; the soft misty rain that had started out the day had started to turn into a light drizzle. He'd only been to Earth a few times in his short life but already Troy had decided that he didn't like it very much. The weather was always changing and unpredictable and it was crowded way too crowded for his liking, he didn't understand how anyone could live there. Earth was a nice place to visit but was somewhere Troy hoped he would never have to live - he would take living in Atlantis any day._

_Troy still didn't understand why they'd had to come back to Earth to have a funeral for his mom when they'd already spread her ashes over the ocean on Atlantis. All they were doing on Earth was burying an empty box. Kate had tried to explain it to him, that it was so the rest of his mom's friends and family - the ones who lived on Earth and didn't know about the Stargate - could have some closure too._

_He glanced up at Rodney who stood next to him one arm wrapped around his shoulders while he held a sleeping three year old Nathan with the other one to see if the rain was starting to bother him too, but the look on Rodney's face told Troy that the man was too preoccupied with other things to notice the rain._

_Next Troy looked over at Kate who was standing on his other side, one hand resting on his shoulder fingers intertwined with Rodney's. Seeing the tears in her eyes Troy reached an arm up to wrap around her waist in an attempt to give some comfort. Giving a sad smile she freed her hand from Rodney's and started soothingly running it through Troy's hair before turning her attention back to the podium. _

_Following her gaze Troy spotted his father, dressed in his dress blues, standing at attention slightly behind and to the side of the President who was standing at the podium giving a speech. That had surprised a lot of people when the President had taken time out of his busy schedule to come pay his respects. Of course those people didn't know about the Stargate at all and therefore had no idea just how important his mom really was; they all just thought that she was an accomplished diplomat._

_He could see Carson, Teyla, Ronon, Radek, and a number of other Atlantis personnel scattered about the crowd as well. The crowd was completely silent as the President finished his speech and stepped back from the podium. It surprised Troy when he felt his eyes starting to tear up when the coffin was lowered into the ground - he hadn't thought this would effect him, that he had gotten through all the crying and stuff at the service they'd had for his mom on Atlantis._

_Shortly after, the crowd began to move off back to their cars, soon leaving only him and his dad standing by his mother's grave. Not missing the way his dad refused to look at him Troy - not wanting to deal with the odd way his dad had been acting towards him the last few days - decided it was time he left and let his dad have a moment alone. Turning he walked away finding his way over to where Rodney and the others where waiting for him._

Seeing the pain and anguish that filled Troy's eyes Elizabeth nearly felt her heart break. Wishing that she could take all of his pain away and shelter him from every bad thing that had ever happened to him Elizabeth wrapped an arm around Troy's shoulders, pulling him close. The two sat there silently watching the horizon until Elizabeth was called back to work.


	6. Changing History

Definite spoilers for '_Allies'_ in this chapter. Italicized dialogue is taken directly from the episode

* * *

Later Troy sat on his bed in his darkened quarters attempting to meditate the way Teyla had taught him when he'd been a child. He could hear the faint hum, the almost whisper of Atlantis in the back of his mind. When he'd been a kid growing up in the city he'd never really been consciously aware of the connection he'd had with the city; the energy, the almost whisper, the way Atlantis was alive in it's own way - not quiet sentient, but more than just an inanimate object. 

He remembered how after Atlantis had been destroyed, he'd felt like a part of him had been viciously ripped out, leaving a gaping hole in his being. But here in this place in this time, that hole had been filled, he was whole again. Yet at the same time he felt lost and alone, like he literally had the weight of the world on his shoulders.

With a sigh as heavy as a stone Troy gave up on trying to meditate and began to pace. He had a huge decision to make that would have long lasting and far reaching consequences and a very small window of time in which to make it. He had been debating with himself for days over whether or not he should interfere with the timeline or just leave it alone. The same thought kept running through his head; Jamas had been right about this being a chance to stop the Wraith getting to earth.

Stopping to look out his window at the ocean Troy rested his head against the cool glass and let himself just listen. He could feel the humming rightness of Atlantis inside his head, lulling and promising, smoothing the edges of his worry and anger. Telling him he belonged here; he'd come home again. With a sudden clarity about what he had to do Troy pushed away from the window and went to grab his combat vest off the chair he'd dumped it in.

Sitting back down on the bed he carefully began to pry apart the lining of the vest. Cautiously he pulled out the two items that he would vitally need if he had any hope of pulling off what he was about to do. The first item was a small canister filled with a substance that was one hundred percent lethal to the Wraith, but completely harmless to humans. The substance was a combination of parts from Carson's retrovirus and parts of the Hoffan serum. By the time the substance had been perfected the Wraith had already attacked earth and destroyed most of earth's defense ships leaving the humans with no way of distributing the drug on a large scale, but even so all off world personal carried a canister with them just in case.

If Troy could place the canister in the right place there would be just enough substance to take out an entire Hive ship. That's where the second item came into play; a Sodan cloaking device. With the cloak Troy would be able to move around the Wraith Hive ship undetected, all he had to do was find away to get aboard the ship.

* * *

Breaking into the Jumper Bay, Troy made a mental note to remember to thank Radek for teaching him everything he knew about the Jumpers. After boarding one of the Jumpers he used his PDA to hacked into Atlantis' system and open the bay doors without alerting anyone in the control room. Cloaking the Jumper Troy set a course for the hive ship. 

Once on board the Hive ship Troy activated the Sodan cloak and silently made his way to the section of the ship that held the life support system. In one of the corridors he came across Ronon, Rodney, and one of the Wraith scientists. Pausing for a moment with his back pressed up against the wall he watched as the Wraith put its hand on Rodney's shoulder. Instantly Ronon grabbed the Wraith and slammed it against the wall, holding a knife to its throat.

_"Ronon, are you crazy? Do you wanna get us killed?" _Rodney's gazed shifted around nervously.

_"You don't touch him." _Ronon growled out at the Wraith.

Trusting that Ronon had things under control and wasn't about to let anything happen to Rodney, Troy continued on his way. Reaching the life support system he worked quickly to get the canister positioned inside the system that scrubbed the CO2 from the ship's artificial atmosphere and redistributed it as breathable air to the rest of the ship. After setting the time delay release Troy took care to leave no trace that he'd been there and made his way back to the cloaked jumper in the hanger bay.

* * *

_"I should be on that hive when we do this."_ Rodney stated as the Wraith queen left the briefing room to return to her ship. 

Watching the queen leave, Elizabeth turned around a look of surprise on her face at Rodney's statement, _"Excuse me?"_

_"Really?"_ John was just as surprised.

_"I know it's uncharacteristically brave, but I've hacked a lot of their systems under the guise of repairing them. I've convinced them that I should be there to supervise their systems if anything goes wrong."_

_"And they agreed to this?"_ Elizabeth was sceptical about the Wraith doing something like that with out an ulterior motive.

_"Yes. Plus, now we can freely beam stuff on and off their ships ... "_ Rodney took a small device out of his pocket. _"...I've written a program that will immediately beam me out of there the second I activate this emergency transponder."_ He smiled proudly as John folded his arms doubtfully.

_"You're sure you wanna do this?"_

_"Of course I don't wanna do it! I just ... I think it should be done."_

_"Ronon goes along."_ John insisted.

_"Wouldn't have it any other way."_ Rodney wasn't entirely happy with that, but knew it was John being John.

_"And I'd like you on the Daedalus."_ Elizabeth turned to John.

_"No place I'd rather be."_

_"OK, good. Let's get this done. I'm about ready for our house guests to leave." _She was about to say more but was cut off by what sounded like gun shots coming from the gate room. Sharing a brief glance with John and Rodney, Elizabeth hurried out of the briefing room to find out what was going on, the two men followed after her. The three reached the small balcony over looking the gate room just in time to see Troy seemingly appear out of nowhere, his P-90 pointed at the Wraith Queen.

* * *

Sodan cloak still active, Troy skillfully maneuvered his way through the city from the jumper bay to the gate room. Finding an out of the way place where he could see the briefing room doors, Troy waited for the Wraith to exit said room. 

He didn't have to wait long. Once the Wraith were out of the briefing room and had been escorted down the large staircase to the gate room, Troy, using the element of surprise, quickly opened fire on the two Wraith guards. Satisfied that they were down and not getting back up Troy de-cloaked and aimed his P-90 at the Wraith Queen. He ignored the soldiers on guard duty who all had their own weapons aimed at him as well as his parents and Rodney, who he could see out of the corner of his eye, his attention solely on the Wraith in front of him.

"What is the meaning of this?" The Wraith Queen, startled at the sudden appearance of Troy, demanded as she discretely moved to activate the transmitter on her wrist.

"Don't bother." Troy spoke up, knowing what she was trying to do. "As of..." He tilted his wrist to look at his watch, "This moment every Wraith on your ship is dead or will be momentarily. There's no one up there to give away Atlantis. You're all that's left of your crew."

"What do you think you're doing Major?" Elizabeth questioned as she reached the gate room level, John right behind her.

"Stopping the Wraith from learning the location of earth." Troy never took his eyes off the queen, so didn't miss the way her eyes slightly widened in surprise. "Yeah, you heard what I said. I know all about your little plan."

"I don't know what you're talking about." The queen couldn't hide the glare in her eyes.

"Bullshit!" Troy fired a single shot into the Queen's shoulder; painful but non-lethal. This of course caused the soldiers to all tense up even more and tighten their grips on their weapons even tighter, ready to react.

"That's enough." Knowing that he wouldn't hurt her, Elizabeth moved in front of Troy to keep him from trying to shoot the Wraith queen again. After ordering the guards to escort the Queen to a holding cell until she had things sorted out Elizabeth turned her attention back to Troy.

The Wraith Queen wasn't happy in the slightest bit about being locked up and would have protested or even fought back, but she knew she was out numbered. Plus if the young man before her was telling the truth, she really was the only one from her ship still alive, there would have been no point in fighting back. Even if she could have gotten away there would have been nowhere for her to go.

Once the Queen was out of the room Troy handed his gun over to John, knowing the man would be even less likely to listen if he was armed. Without a word Elizabeth turned and headed back to the briefing room, John and one of the guards that had remained ushered Troy after her. In the briefing room John and Elizabeth sat at one end of the table while Troy sat at the other.

"So you gonna tell us what that was all about?" John asked, arms folded and a scowl on his face.

"Should probably get the rest of your senior staff in here first. Save the trouble of having to go over this more than once." Troy leaned back in his chair nonchalantly. At this point he had nothing to hide. He'd just changed history after all, pretty much everything he knew was moot at this point.

Agreeing Elizabeth called Carson and Rodney over the radio and asked them to come to the briefing room. Rodney was there almost instantly, having been hovering around in the control room, Carson took a few more minutes to get there. Once they were all there and settled she turned her attention to Troy. "Now why don't you start from the beginning."

"First, everything I told you about how I got here and all that stuff was true. I didn't come here with the intention of changing history, but I realized that Jamas was right about this being a chance to stop a war, to save billions of lives. His way of going about it may have been wrong, but not the idea. The Wraith never had any intention of forming a legitimate alliance with you. The alliance, their willingness to share information, all of it was nothing more than a ruse to learn the location of earth."

"How?" Elizabeth began to get a sinking feeling in her stomach at how close she'd come to allowing the Wraith access to earth. No matter what anyone said if the Wraith had managed to learn the location of earth it would have been her fault and her fault alone, she was the one who had agreed to Michael's proposal.

"The information they downloaded to you. Within the hive ship's schematics was a worm-like computer virus. Unfortunately the virus wasn't detected until after the Daedalus and the Hive ship, with Rodney and Ronon on board, had already left Atlantis this last time."

"What was this virus designed to do?" Rodney was curious. They'd gone over the Wraith downloads with a fine tooth comb and found nothing.

"It very selectively probed Atlantis' systems without damaging them or exposing itself. Once the hive left Atlantis, the worm began to destroy all of the data they had sent down. It uploaded two pieces of information: one – the Aurora mission reports...and two...the location of every world in your database. Which as I'm sure you all know includes earth."

"Luckily you were able to rescue Rodney and Ronon and destroy the hive ship before it reached earth, but unfortunately not before they were able to transmit earth's location to other nearby ally Wraith ships. Thankfully for us they didn't go after earth right away, they were all to busy fighting each other in their little civil war."

"It was another five years before the Wraith started to show up in any real force in the Milky Way galaxy. Every once in a while during those five years a ship or two might've showed up but it was nothing that couldn't be handled by either earth, the Asgard, the Tok'ra, or the Jaffa. Then something changed, the Wraith stopped fighting each other, whether that was because one side had come out victorious or they finally got their acts together and stopped fighting to team up, I don't know."

"We were able to hold our own in the beginning, but it wasn't enough. Nine years after they started really showing up in the Milky Way, when I was fourteen, the Wraith managed to find away around Atlantis' sensors and catch the city off guard in a surprise attack. We were forced to evacuate back to earth when it became obvious that the city was lost."

"Another six years after that the Wraith finally broke through earth's defenses and devastated the planet. Out of the billions of people on earth only a little over a thousand managed to make it to safety. We've been on the run ever since."

Finished giving a basic run down of what the last twenty-four years had been like, Troy paused a moment to let everything he'd said so far sink in.

"How were you able to kill all those Wraith on the hive ship?" John inquired after a moment. Out of everything that had happened so far he found that it was surprisingly that question that had been nagging at him the most.

While they'd been waiting for Carson, John had contacted Caldwell and had him run a sensor sweep of the hive ship. The colonel had confirmed that there were no life signs that could be detected - which didn't really mean anything since hibernating Wraith didn't show up as life signs. So far all the teams that had been sent over had found nothing but dead Wraiths everywhere.

"Airborne contagion that Carson and some other scientists developed, using a combination of parts from Carson's retrovirus and parts of the Hoffan serum. It's one hundred percent deadly to the Wraith, but completely harmless to humans. "

"One hundred percent?" Carson spoke up for the first time, not liking what he'd just heard. He was already having issues with his conscience and morality over the retrovirus he'd developed to turn Wraith into humans...but genocide? No he would never allow himself to go that far...would he?

"Yeah, unfortunately for us by the time the substance had been perfected the Wraith had already attacked earth and destroyed most of earth's defense ships leaving us with no way of distributing the drug on a large scale. All off world personal carry a canister with them just in case they're captured though."

"No, I can't believe that I would willingly participate in what essentially amounts to genocide. When I developed the retrovirus for the Wraith, it was to free them from what I perceived to be an unnatural state, not kill them."

"You say that now, but I guarantee you, that you stopped giving that bullshit answer after you were forced to watch as your _wife_ and _daughter_ where taken and fed upon right in front of you, during that last attack on the city by the Wraith." Standing up Troy began to pace. "Every _last_ one of us who survived that last attack changed, including you Carson. We all changed into people we never wished to become, did things we're not proud of, but we did it in order to survive, to keep the Wraith from destroying _us_."

Having nothing more to say Troy turned and left the room, the others were too stunned by everything they'd learned to try and stop him. He could feel all the emotions he struggled to force down everyday threatening to surface and consume him. He had to get out of there and regain his balance before he drowned in the emotional tidal wave he'd been riding since being thrown back in time.

* * *

Later that night Elizabeth sat up in bed leaning against the headboard, her knees pulled up to her chest, arms wrapped around them. Resting her chin on her arms she listened to John's soft breathing as he slept next to her. She longed for the comfortable embrace of sleep, she couldn't remember the last time she'd had a decent, honest to goodness night's sleep with out the aid of the sedatives Carson had prescribed for her. And even those weren't as affective as they once had been. 

Her mind was racing with thoughts of the day's events, what had happened...what could have happened. When she thought of what would have happened if it hadn't been for Troy, of all the lives that would have been lost because of her decision - and it was her decision no matter what anyone said, in the end she always had the last say - it made her want to curl up into a tiny ball and just dissappear. An incredible feeling of overwhelming hopelessness and guilt threatened to drown her in its intensity.

Drifting into wakefulness John's sleep fogged brain registered that something was slightly off around him. Peeling an eye open he made out the shape of Elizabeth beside him, sitting with her back against the headboard and her knees drawn up. Immediately he knew something was wrong, carefully, not sure if she was aware that he was awake, John reached out to gently rub a hand up and down Elizabeth's shin.

"What's wrong?" John hated seeing her upset or hurting in any way.

Elizabeth was silent for several moments before answering, "I don't think I can do this any more."

Really worried now John sat up, wrapping an arm around Elizabeth's shoulders, his other had rubbing up and down her arm. "Do what anymore?"

She looked up, frowning like she'd expected him to know the answer to that. "This job. I don't think I'm cut out to make the kind of decisions it requires.

"Why would you thing that? You're great at your job, sure sometimes it can suck like hell, but I don't know anyone I'd rather have doing it." Kissing her temple softly, John started to soothingly rake his fingers through her hair. "Does this have something to do with what happened today?"

"God, John when I think of what would have happened if it hadn't been for Troy, of the lives that would have been lost..." She couldn't fight it off anymore, Elizabeth buried her face in John's shoulder and let the tears she'd been fighting back fall.

"Shh...I know, I know." John pulled her close, rocking gently. When her tears subsided he pulled back just enough to look her in the eyes. "Elizabeth you're one of the strongest, most compassionate people I know, and believe me when I say there is no one who could have done a better job here than you have."

"You can't beat yourself up over something that didn't happen...not this time anyway. Troy changed history, changed the timeline, the things he spoke of might still happen or they might not, but the fact is that's all in the future and we have no way of knowing what'll happen. But whatever happens we'll deal with it together when the time comes, until then all that matters is the here and the now. We just take it one day at a time, whatever's meant to happen will happen." Adjusting their positions so that they were laying down - her on her back and him on his side - John wrapped an arm around Elizabeth's waist pulling her close to him. "Now come on you need your sleep. All this worrying and stress can't be good for the baby." He bent down to lovingly kiss her stomach before settling back.

Knowing that John was right Elizabeth let out a soft sigh as she snuggled into John's warmth, grasping the hand that rested on her stomach, entwining their fingers together. Tomorrow was another day, another chance to try and make things better. She could live with that...for now.


	7. Breaking Point

A/N: Ok just to be on the safe side, I'm putting a language warning on this chapter. I've also been advised that a tissue warning might be a good idea, but I'll leave that up to you to decide.

* * *

A week later, standing on his favorite balcony Troy leaned against the railing taking in the view. Despite the virtual geekasims they were having at now having an intact and fully functional Wraith hive ship at their disposal, Rodney and the other scientists had managed to finish building the generator and were doing some last minute testing and calculations. 

By this time tomorrow Troy would be on his way back to his time period and just incase he got back and things hadn't changed, Atlantis was still destroyed and earth was still lost, or things were worse than they had been, he wanted to have the image before him burned into his mind so that he never forgot it.

Hearing the balcony doors open he didn't turn around figuring it was his mom since no one else knew that he liked it out there better than anywhere else.

"Can we talk?" Troy tensed up straight at hearing John's voice. Knowing that time was running out and that Troy would soon be gone John had decided to make another attempt at trying to fix things between him and his son - if only he knew what exactly it was he was trying to fix.

"I got nothing to say to you." Troy's tone was clipped.

"I think you do. Quite a bit to say, actually." John moved over next to his son, back against the railing.

"What do you care?"

"I care a lot. You're going to be leaving soon and I don't want things to be the way they are between us right now." He paused to scrub a hand through his hair. "I guess...I just...I don't like the fact that you grow up to hate me. I've technically only known you a few weeks, but the fact is you're my son and I care about you."

That was it, something snapped inside Troy. He couldn't hold it in any more. Pushing off the railing he stormed away a few steps putting some distance between them before whirling around to face his dad, fury flashing through his eyes. "You never gave a rat's ass about me! Not since I was six years old and mom died!"

"When she died it shattered you, completely destroyed you. I reminded you of her so much, of the pain you felt at loosing her, that you couldn't even stand to fucking look at me. Hell you could barely stand to be in the same fucking room as me! You buried yourself so far into work that sometimes it seemed like you forgot I even existed. Your job, this city, and everyone else in it _always_ came first to you. I remember people used to tell me that things would get better, that you were just grieving, I just had to be patient, but you know what? It never fucking did!"

"Growing up it seemed like the only time I ever got _any_ kind of attention from you was when I was in trouble and you were yelling at me! It got to the point where I purposely got myself in to trouble just so I could get some attention from you. But after awhile even that stopped working. You just couldn't deal, you gave up on me, stopped trying...stopped fucking caring."

"The only reason I am the man I am today is because Rodney stepped up to the plate when he didn't have to and acted more like a father to me than you ever did. Shit the only reason I'm even alive today is because Rodney cared enough about me to be there for me _no matter_ what. I mean shit you have no idea how many times I actually thought about fucking ending it when I was a kid, just throwing in the towel and making the pain and the anger go away permanently. The only reason I never did was because I knew that Rodney was there for me, that any time I needed him, day or night, he would be there. Also I never did it because I didn't want to be like you. Ending it would have meant abandoning those that care about me, the way you abandoned me, just without the dying part, and I never wanted any of them to feel the way that I did..."

Feeling like he was about ready to beat the shit out of John again Troy stopped and turned to leave but something made him stop in the doorway. He had one last thing to say, "When the Wraith destroyed Atlantis, it was Rodney I grieved for, not you." The last bit was whispered so softly Troy wasn't even sure he'd spoken it aloud.

John was speechless, he had no idea what to say. Of all the things he'd expected to have happened between him and his son, none of the things Troy had just said made the list. God he'd become his own father, treated his son the way he'd been treated, the way he'd sworn to himself he would never treat his child. Thinking things couldn't get any worse John nearly recoiled backwards as if he'd been hit when he heard Troy's whispered confession in the door way.

"What can...? There has to be...something I can do to change things...between us." John, choked out, finally finding his voice. "A way to fix things."

"Last time I checked you couldn't stop people from dying or bring them back from the dead. So I seriously doubt that there's anything you can do to 'fix things'." With that Troy left the balcony.

Now even more determined to make sure things turned out differently John watched as Troy stormed off. His son may have been convinced that it was hopeless, but to John that future hadn't happened yet, there was still a chance to set things right. Even if he had to die trying John swore to himself he would do whatever it took to fix his family.

* * *

Anger burning through him with a fury, Troy barely made it back to his room before he lashed out. Rage boiled inside him, feeling like it would burst his chest open if he didn't find away to release it. He'd reached his breaking point; all the rage, anger, and a million other emotions he couldn't name exploded to the surface like an erupting volcano. 

Grabbing the nearest item - a wooden chair - Troy slammed it into the wall, barely noticing as it shattered. Next went the Ancient's version of a lamp from off the bedside table, the table itself soon followed. The bed was launched onto its side, more tables and chairs were smashed; throwing, smashing, kicking, hitting, Troy did it all to what ever came with in his reach as the rage consumed him. Troy barely felt the glass that savagely tore deep into his wrist as he smashed his mirror - the last item left untouched in his rampage. His room destroyed Troy, still needing an outlet for his fury, fled the room and soon found himself in the gym.

Not bothering to wrap his hands or put on gloves, Troy began to ruthlessly batter the poor punching bag. Bone jarring hit after bone jarring hit, rattled the chains holding the bag up. Amongst all the rage, anger, and pain he felt something swell to the surface, something he'd never fully allowed himself to feel; a soul searing sorrow that cut through to his very core.

Giving one last bone shattering hit, Troy felt the punching bag rip open, spilling its stuffing out on to the floor. With the bag no longer providing resistance his momentum carried him forward, spinning him around slightly, slamming his back into the wall. Tears sliding down his face Troy slid to the ground, drawing one knee up wrapping an arm around it and resting his head there. Sitting there struggling to suck in enough air to his oxygen starved lungs, Troy was reminded of a poem he'd once heard, thinking of it now he found it ironically fitting.

_Darkness boils in my blood  
Its hot, bubbling anger oozes out of my pores.  
I feel its need for absolute vengeance,  
The fire is inside me, ravaging at me,  
Plundering at my mind, obliterating my own thoughts.  
The hell storm takes over;  
I have become one with Darkness.  
I am my own shadow nemesis;  
I am the Dark Reprisal.(1)_

* * *

He had no idea how long he'd been sitting there before he felt someone - he guessed Teyla by the silent and graceful footsteps - slide down to sit next to him. Troy didn't lift his head or acknowledge her in any way and she remained silent for several moments. At the sight of the trashed punching bag and Troy slumped against the back wall it hadn't taken Teyla long to figure out that the anger simmering inside of Troy had finally reached its boiling point. 

Due to circumstances beyond her control Teyla had not been able to spend as much time with Troy as she would have liked, but from what little interaction she'd had with the young man Teyla could tell that he'd lived a life of hardship, filled with more grief and anger than joy and happiness. She could see inside him a burning rage, much like the one she could see in Ronon towards the Wraith, when they'd first met. With the release of his rage, Teyla hoped Troy would now begin to heal.

Troy gave a soft humorless laugh, breaking the silence first, "Marcus Antonius once said: 'Consider how much more you often suffer from your anger and grief, than from those very things for which you are angry and grieved'."(2) He quoted the Roman politician and general as he moved his head back to rest against the wall.

Teyla didn't know who this Marcus Antonius was, but she did have to agree with his words. "It sounds like this Marcus Antonius was a wise man. I would be interested in hearing more."

"Not sure everybody would agree with you, but to each there own. As for the hearing more, talk to someone in the archaeology department, they'd know more than I do." The two fell silent again.

"Some times when we are angry we have every right to be so, but we must remember that, anger is a killing thing: it kills the man who angers, for each rage leaves him less than he had been before - it takes something from him."(3) Teyla stated softly, breaking the silence this time, remembering the words her father had spoken to her when she had been a child.

"That you're subtle, round-about way of telling me I have to let go of my anger before it destroys me?" Troy didn't wait for an answer, pushing himself to his feet. "Well I gotta tell you it's not as easy as you might..." He trailed off as he suddenly felt lighted headed and was it just him or had it suddenly gotten cold in the gym?

Seeing Troy waver on his feet Teyla quickly stood, wrapping one arm around his waist and gently grasping his elbow with the other. As she steadied Troy it was then that she noticed the large amount of blood that was dripping from the finger tips of his right hand. Carefully, but with a sense of urgency, Teyla lowered Troy back down to the floor. Examining his arm closer, she found a decent sized piece of glass lodged into a heavily bleeding, jagged gash on his wrist. The last thing Troy was aware of before being pulled under by blackness was Teyla calling for a med team.

* * *

(1) - Poem is by Sylvia Wei (at least I hopes that's right. I found it on the internet so it's possible I could be wrong). 

(2) - Quote from Marcus Antonius (more commonly known as Mark Antony), an important supporter of Julius Caesar and acknowledged lover of Cleopatra.

(3) - (Anger is...) Quote from Louis L'Armour


	8. Truce

_"Defense perimeter has been breached. Wraith armada inbound, ETA earth orbit one hour." _

"_Orbital Cannons in position. The Daedalus, the Odyssey, and the Orion holding in orbit."_

_"Ancient outpost powered, drones ready to fire."_

_"We have contact, Wraith armada is exiting hyperspace. Squadrons of Darts are being launched."_

_"F-302 squadrons launching."_

_"The enemy has been engaged."_

_"Odyssey has been destroyed and the Orion is severely damaged."_

_"All the remaining F-302s have expended their ordnance."_

_"The Ancient outpost has taken a direct hit."_

_"Enemy troops have landed."_

Jerking awake Troy, heart pounding, bolted up right in bed. His body reacting before his mind could clear out the fogginess of sleep, he swung his legs over the side of the bed and reached under his pillow for the hand gun he kept there...only there was no gun. That confused Troy, he always had a hand gun under his pillow.

"Easy lad, it's alright. It was just a bad dream." The familiar accent registered in Troy's mind, as he felt hands brace his shoulders, keeping him from completely bolting off the bed.

"Carson?" It took a second for his mind to catch up and realize that he was in Atlantis in the past and not on earth during the Wraith attack.

Tension easing from his muscles Troy slouched back slightly, putting his right hand down to support him. He winced when pain shot up the arm. Lifting it back up he frowned in confusion at seeing his wrist wrapped with white gauze. His head felt foggy and for the life of him he couldn't remember how he'd gotten hurt. The last thing he remembered clearly was being on the balcony with his dad after that things got hazy, it was mostly just feelings; intense rage, anger, sorrow, and something about Marcus Antonius. Troy mentally shook his head, he didn't even want to know how that last part fit in.

"Troy?" The sound of his Carson's voice brought him out of his thoughts.

Looking up from his bandaged arm Troy looked first at Carson, then his mom who was standing next to Carson, "What happened?" He indicated his arm.

"What's the last thing you remember?" Elizabeth questioned, while Carson busied himself checking Troy's vitals.

"I was talking to dad, but after that everything gets fuzzy, kinda like I've been on a weekend long drinking binge with a bottle of Radek's hooch." Troy didn't miss the way his mom raised an eyebrow, a hint of disapproval in her eyes. He ignored the look he was a grown man and of legal age to drink. after all. "Mind filling me in on the rest?"

"Well it seems for whatever reason, you decided to destroy your quarters and in the process you managed to slash your wrist open on the mirror you smashed."

"And of course instead of seeking proper medical treatment you went to the gym. While there you literally beat the stuffings out of the punching bag, which lodged the piece of glass stuck in your wrist deeper into your arm." Carson added, obviously not pleased. "It was a close one, if Teyla hadn't been there you very well could have bled to death."

Thinking about it for a minute, it suddenly all came flooding back to Troy, everything that had happened. "Actually doc it was probably a good thing that I didn't come here after trashing my room. With the mood I was in I probably would have ended up trashing this place as well. And I'm pretty sure a punching bag is easier to replace then some of the stuff in here." He ran a hand through his hair, "When can I get our of here?"

Definitely his father's son, Carson thought as he let out a soft sigh, "Everything looks to be alright, so I suppose you can go now." You didn't have to be a rocket scientist to see that the man wasn't completely thrilled with the idea, but had no real legitimate reason to keep him there. "I'll go get your close."

Looking down it was then that Troy noticed that he was wearing scrubs, "How long have I been here?" He asked as Carson left.

"Since yesterday afternoon." Elizabeth answered as she moved to sit next to Troy on the bed. "We should talk."

"About what?" He didn't think there was anything to talk about. So he'd had one little freak out, it was no big deal.

"About what happened yesterday, about why you went on your little rampage." John had told her everything about his conversation with Troy the day before, but she wanted to hear her son's side of it.

"What's the point? It's done and over with. Besides I think everyone's entitled to a freak out every now and then."

Elizabeth was about to speak but paused, her eyes going slightly wide and her hand going to rest on her stomach. She was around five months pregnant now and it was beginning to show. The hand stayed in place for a moment before moving slightly to the left.

"What...what is it? Are you ok. should I get Carson?" Troy slid off the bed and was about to go after Carson when Elizabeth grabbed his uninjured arm, moving the hand to rest on her stomach where here hand had just been.

It wasn't long after that, that Troy's own eyes went wide. "Is that...?"

"Yeah, that's you moving around in there." Elizabeth couldn't keep her grin from growing at the wide eyed wonder on her son's face.

Troy suddenly jerked his hand back, realizing that yes that was _him_ moving around in there. "Ok that was just weird, even for me."

Returning with Troy's clothes Carson was just in time to see the younger man jerk his hand away from Elizabeth's stomach. Setting the clothes on the bed he raised a questioning eyebrow towards Elizabeth.

"The baby moved," was her explanation.

"Finally?" Carson held a hand out stopping just short of her stomach, silently asking permission. Elizabeth nodded her head taking Carson's hand, placing it where she could feel the baby moving.

Using their moment of distraction Troy quickly grabbed his clothes from where Carson had laid them and high tailed it out of the infirmary. He didn't know where he was going to go - his balcony was out of the question, that would be the first place his mom went looking for him - but he had to get away from there, away from the conversation his mom had been trying to have with him.

After briefly ducking into a supply closet to change out of his scrubs, Troy just started walking letting his feet take him where ever they pleased. It was with only a small amount of surprise that he ended up in the Jumper Bay. He loved flying, especially the jumpers - it was one of the few things he and his dad had in common, although they'd never really done it together - so it only made sense that he would end up there.

Boarding one of the jumpers Troy sat in the pilots seat, he was tempted to take the jumper out for a flight but with out his PDA to hack into Atlantis' system, his departure would alert the control room, which was the last thing he wanted. So he just sat there and let his mind wander back over all the good memories he had of flying. He couldn't have been there more than twenty - thirty minutes before he heard someone else enter the jumper bay.

"For what it's worth, I'm sorry. I know that doesn't mean a whole lot to you, but I am." Troy didn't look at his dad as the man boarded the jumper, stopping in the bulkhead doorway. "I'm sorry that I was such a lousy father to you, I'm sorry I treated you pretty much the exact same way my old man treated me."

Troy remained silent, absently fidgeting with the jumper controls. John was at a loss for what to do. When he'd been informed that Troy had taken off from the infirmary before Carson had 'officially' released him, John had just instinctively known to check the Jumper Bay. It was were he would have gone to try and think things through, to try and clear his head.

"Look Troy, I...I'm not good with the whole deep emotional thing, never had been. So could you help me out here, tell me what I have to say or do to set things right. Cause, you know I gotta tell you I'm flopping hear, I have no clue what to do."

Troy still remained silent, but had stopped fidgeting with the controls, that was something at least.

"Please say something, anything, I don't care what. Yell at me if you want...just...just say something, please."

There was a moment of silence before Troy lifted his head up, "It wasn't entirely your fault." He finally whispered.

"What?"

This time Troy actually turned to look at his dad. "It wasn't...this rift between us...it wasn't entirely your fault." He dropped his gaze again. "You're not the only one who gave up. After a while I...I just got so fed up with having to work my ass off for every tiny scrap of attention I got from you that I just stopped trying. I left you to your grief and pain, the way you left me to mine."

"So what do we do now? How do we fix this?" John moved to sit in the co-pilot's seat.

"I don't think there is anything that we can do. It's too late for us." Troy paused at the crestfallen look on his dad's face."But just because there's nothing you can to do fix things between you and _me_ doesn't mean you can't fix things between you and _him_."

John didn't need to ask who 'him' was...him...the baby currently growing inside of Elizabeth, the baby that would grow up to be the young man in front of him...and yet not at the same time.

Taking the words for what they were - a truce - John gave a slight nod, turning to the controls in front of him. "What'd ya say we take this thing out for a flight? I hear Rodney's the one who taught you how to fly." He couldn't help the small sarcastic smirk.

"Hey, lay off the man. He's not that bad of a pilot...once you get past the whole flying in a straight line thing." Troy also turned to the controls, starting to run through the pre-flight checks.

Before long the two were soaring through the sky headed for a low orbit around the planet and John had to admit the kid was a pretty dang good pilot...who knew Rodney had it in him to be a good flight instructor?

* * *

The next day everything was set and ready to send Troy back to his time period. Standing in the gate room staring into the faces of his family Troy wasn't sure how to say goodbye and by the looks of it neither did they. 

It was Teyla who finally made the first move, placing her hands on his shoulders and bowing her head, " May the Ancestors always watch over you."

"And they you." Troy returned the gesture touching his forehead to hers.

Ronon was next, he didn't say anything just held out his hand, which Troy gladly took. Neither man needed to say anything, they both knew that in away this wasn't goodbye, just a 'til next time.

After Ronon came Carson, "Take care of yourself lad."

"You too Carson." He hugged the man. Next he turned to Rodney, giving the man a hug as well. "Don't let my dad give you a hard time about flying. You're just as good as him, you just have to have confidence in your abilities." Troy whispered into his surrogate dad's ear.

When his mom hugged him, Troy actually feared the woman might break one of his ribs. Pulling back he placed a hand on her stomach, still feeling a bit weird about the fact that he could feel himself moving around in there - but then again it could have been worse, he could have been around after the kid was born and need a diaper change; that would have been too much. "Stop worrying about everyone else so much, they're big kids, they can look after themselves. You need to take better care of yourself more often."

She didn't bother to ask him to clarify, she'd given up on trying to get details like that from him. "I would tell you to keep out of trouble, but it wouldn't do any good." She smiled, "Because whether you like it or not, you are your father's son."

Normally Troy would have bristled at such a comment, but after the last few days he had to admit that, yeah maybe he was a _little_ bit like his dad. Speaking of which he turned to said man holding out his hand; they weren't quite to the hugging stage. "Don't screw up, you might not get a third chance."

"Not planing on it." John returned the hand shake, then stepped back a step and saluted his son. Troy immediately returned the salute. In that moment something passed between the two men - an understanding of some sort. With a final glance over his shoulder, Troy turned and walked through the rippling gate.

* * *

A/N: Ok only one maybe two more chapters left (I have two possible epilogue ideas bouncing around in my head and might write them both out). 


	9. Epilouge Version One

A/N: I have decided to do both versions of this story's ending. This is version one, it's kind of sadder yet not at the same time, than my other version which is happier. I'll let you guys decide which one you like better.

* * *

Slowly Troy became aware of the sound of someone moving around in the small kitchen unit of his quarters, followed by the scent of sausage penetrating his nose. It had to be his dad making breakfast, ever since Troy had been a kid and his mother had passed away his dad had insisted on the two of them having breakfast together _every_ morning; the fact that his son was a grown, twenty four year old man and living on his own didn't stop John from breaking into his son's quarters every morning, just so they could have breakfast together - said a son was never too old to spend some quality time with his old man. 

Groaning he burrowed deeper into his covers, it couldn't be morning already. It felt like he'd just gone to bed, which wasn't entirely untrue; the day before Troy's team had been on a planet where the day and night cycles were opposite of Atlantis', which meant they'd returned home during the night - Atlantis time. When the whistling started he shoved his head under his pillow wondering if he could get away with suffocating himself. His dad had no business being that chipper in the morning...

...His dad...?

Suddenly without warning memories of another life time assaulted his sleepy mind. Memories of a lifetime full of sorrow and anger, memories of Atlantis being destroyed, of the Wraith attacking earth, all merging with the memories of his life in this timeline. Staggering out of bed Troy bolted from his bedroom into the living room.

Hearing the bedroom door slide open John stopped whistling, "It's about time you got up. I was starting to think I would have to go in there and drag you out of bed. What time did you get in last night...?" He trailed off as he turned around and saw his son.

Taking in his son's pale face, labored breathing, and the conflicting emotions flashing through his eyes John lost the smile on his face and quickly moved to seat his son on the couch. "You remember." It was a statement, not a question.

Both John and Rodney had wondered and speculated about what would happen to the other timeline version of Troy after he'd stepped through the gate nearly twenty five years ago. They had wondered if the first one would just cease to exist, did the two timelines split into alternate realities and the first Troy went to the one where his timeline was still playing out, or would the two versions merge together someway. Looked like he had his answer now.

"Yeah...It's weird, I feel like I've lived two different lives in the matter of seconds." Troy stood up moving to the window. Taking in the ocean view he leaned his forehead against the glass. "I still remember everything from this life, a life where the good and happy far out weighed the bad and anger, yet at the same I also remember living a life where the bad and anger far out weighed the good and happy."

"I remember all the rage he felt towards you...towards everything, but then I remember all the happy times me and you have had together. I remember Atlantis being destroyed, Rodney being...being fed on by a Wraith, the Wraith attacking earth, my going back in time..."

John was at Troy's side in a few quick strides. Not knowing what else to do he pulled his son into a comforting hug. "It's ok, none of it happened. You stopped those things from happening."

"Not everything." Troy pulled back, not looking into his dad's eyes. "I...didn't...I didn't save mom..." He trailed off as a wave of guilt washed over him, he'd failed to change the one thing he'd wanted changed more than anything.

"Hey, look at me," John caringly cupped Troy's face forcing the younger man to look at him. "That was not your fault and I don't ever want you to blame yourself. There was nothing _you_ could have done to change what happened to your mother, you were just a child. If any one should feel guilty it's me. I knew what was coming, maybe not the details, but I knew something was going to happen. But even with that information I still couldn't save her."

"Don't...don't blame yourself. I...he...should have given you more information..."

"It doesn't matter, it's neither here nor there. We can't dwell on what should or shouldn't have happened, all we can do is go on with life the way your mom would have wanted us to. We were given a second chance, let's make the best of it." Moving his arm around his son's shoulders John started for the kitchen. "Now come on breakfast's getting cold."

Troy knew it wasn't going to be that easy to come to terms with all the new stuff bouncing around in his head, but at least he had his dad there by his side to help him through the rough spots.


	10. Epilouge Version Two

A/N: Second more happier ending. Kind of short, but my muse has decided to abandon ship (Good thing it's the end of this story)

* * *

Navigating his way through the crowded corridor Troy entered the control room, spotting his dad standing on the small balcony over looking the gate room. He wasn't surprised to find the man there, his dad had been irritable and edgy all week barely leaving the control for any reason. Not that he could blame the man, Troy had been in a similar mood that whole week as well. 

"She said 13:00, right?" Moving to stand next to the man Troy could tell that his dad was nervous by the way his shoulders were tensed and by the white-knuckled grip he had on the railing.

"That's what she said." John consciously forced himself to let go of his death grip on the balcony railing, his eyes never leaving the gate.

"You guys need to relax," Rodney spoke up from the console he was working at. "It's not like she's never been off world with out one or both of you before." Neither man said anything just glared at Rodney in an obvious 'shut up' look. He shook his head at their over protectiveness.

After what felt like an eternity the gate finally started to activate. Watching as Elizabeth stepped through the open gate Rodney could've sworn he felt the tension literally drain off of Troy and John as both men moved down the staircase to the gate room.

Elizabeth had been off world at a trade conference for the last week, and Rodney had to admit that both Sheppard men had nearly driven him along with half the city to mutiny. The two men had driven Rodney up the wall with their constant hovering in the control room, and their moodiness. So no one was happier than he was that she was finally back.

"Here let me get that." Troy spoke as he moved to take the field pack off his mom's back. Shooting a quick glare Lorne's way as if to say how dare he let his mom carry her own bag.

"You know I am more than capable of carrying a bag." Elizabeth frowned slightly as John gave her a welcome home kiss.

"I know." Troy slung the pack over his shoulder anyway.

Elizabeth just rolled her eyes. She loved her two guys, she did really, but sometimes she just wanted to smack them. Thanks to the two men in front of her - and she knew it was because of them - she'd spent the last week with her very own Lorne sized shadow. Every where she went it had seemed like Lorne was right there hovering. When she'd called him on his behavior, Lorne had reluctantly told Elizabeth everything that John and Troy had threatened to do to him should he let anything happen to her, and having no doubt that they were serious he'd taken their threats to heart. It didn't matter what Elizabeth had tried to tell him the man wouldn't let up, simply stating that John and Troy scared him a hell of a lot more than she did.

For the most part Elizabeth was used to their over protectiveness, both men had been that way for so long it was hard for her to remember a time when they weren't. It had been over _eighteen_ years since she'd nearly died from cancer and they still treated her like a porcelain doll most of the time. She admitted that it had been close, too close, in fact they almost hadn't caught it in time. If it hadn't been for the younger Sheppard - even though he didn't know it - standing before her, they probably wouldn't have caught it until it was too late. It had been a long hard road to recovery for her but Elizabeth had come out on top in the end. In the last eighteen years she hadn't had any relapses but John and Troy still made sure that she always went in for regular check-ups, ate three meals a day, didn't over work herself, went to bed at a decent hour - basically they treated her like a child sometimes.

"So how'd everything go?" John questioned, wrapping an arm around his wife's waist as the three left the gate room.

Giving a small sigh of defeat, Elizabeth let John lead the way while Troy brought up the rear. Yeah sometimes they were annoying, pains in the ass, but they were her annoying, pains in the ass and she wouldn't have it any other way.


End file.
